The advent of genomic analysis has identified regions of functional significance in several mammalian species. However, for horses, relatively little such work was done compared to other farm animals. The current archive of genetic variations in the horse is mostly based on the Thoroughbred mare upon which the reference sequence (EquCab2.0) was generated. Thus, more investigation of the equine genomic architecture is critical to better understand the equine genome. Chapter 2 of this dissertation represents an analyses of next generation sequencing data of six horses from a diverse genetic background. I have utilized the most advanced techniques to identify, and annotate genetic variants including single nucleotide polymorphism, copy number variations and structural variations pertaining to these horse breeds. The analysis discovered thousands of novel SNPs and INDELs and hundreds of CNVs and SVs in each of the horses. These newly identified variants where formatted as online tracks and should provide a foundational database for future studies in horse genomics. Chapter three of the thesis discusses a genome wide association study aimed at the discovery of QTLs affecting body size variation in horses. I used the Illumina Equine SNP50 BeadChip to genotype 48 horses from diverse breeds and representing the extremes in body size in horses. Unlike most association studies, I have utilized a dominant model to identify these QTLs. The analysis revealed an association in chromosome one at the ANKRD1 gene (involved in muscle myocytes and cardiomyocyte growth and differentiation). In chapter four, I represent the results of a genomic study in which 36 Egyptian Arabian horses were genotyped using the Illumina Equine SNP70 BeadChip. The study was conducted to elucidate the genetic background of the herd, relatedness within the herd and to estimate genomic inbreeding values. I was able to re-establish the genetic links between the horses and to confirm their Egyptian ancestry among other Arabian horse bloodlines. Genomic inbreeding values were highly correlated with the pedigree estimated ones. Altogether, our results signify the benefit of using this BeadChip technology to infer relationships within herds and ancestry of herds and to estimate inbreeding in herds lacking pedigree recording.